Welll there's the "temperature" method, where if your main color is a "warm" one (red/orange/yellow/etc) then you choose something with a "cooler" color (blue/green/purple) for the shadows. And vice-versa, I suppose.

And that's pretty much all I know about picking colors._________________

I could be wrong, but I gather most digital artists just create a multiply layer.

You are wrong in that 'most digital artists do this'. It's frequently used for cel-shading because it's fast and can give good results if you don't use black and white! But most digital artists (not just digital comic colorists) hand-pick colors because it gives you greater control.

Using a multiply layer for shadows and a screen layer for highlights is a good fast way of laying down cel-shading but it's a bad habit to get into because it decreases the control you have in the end result.

I frequently suggest launching into more dynamic shading by trying blue or purple for shadows, and warm tones for highlights... that's how things generally are in real life, naturally. And yeah, you can even do this with multiply/screen.

smbhax mentioned the temperature method and it's a great way to add depth. It is a good trick, and definitely the easiest way to start shading with something other than a multiply layer.

Now, I'm not saying don't use layer styles at all... I make frequent use of the linear dodge, overlay, multiply, hard light, hur, color, saturate, basically any layer styles I think look neat for various lighting effects, but I use them strictly for lighting effects after I've done my shading and keep my shading to manual, hand-painted shading. I sometimes apply the lighting effect to the brush in Photoshop, which can be selected in the top bar, because this makes great highlights, for example, or I'll use a color on a multiply layer to deepen shadows, or a color layer transparent to neutralize colors that got really weird.

So, this is more or less how my shading technique works. Here, I make you a tutorial. I'm a painter, but the basic idea can apply to cel-shading too. Basically, transparent everything, pick new colors as you go, you can't go wrong with what colors you pick as long as you pick temperature contrasting highlights versus shadows because even if it looks weird you can fix it with layer styles later. Be confident because honestly, you can't really go wrong!

And oh yeah, I guess you might want this bit of advice because it does answer your question.

Draw a line across your circle and pick colors only from that line. Use one side for the highlights and one side for the shadows.

If you pick colors only in a straight line (warm to cool!) when you're starting out you'll always stick to the warm/cool ideal and always have a decent color pairing. This is "complimentary color theory". Then move on to triangles once you're confident with the basics of warm/cool contrast. You'll notice that I used three colors for shading... the first two were in a straight line across from each other and I triangulated into purple. This was a choice based on the triad color theory.

That's really basic color theory right there. Smack a triangle over a color wheel and pick what you like. Sites like this will help you visualize it and can be a handy way to launch into picking colors to start with. http://colorschemedesigner.com/_________________